Compact phases of polymers with hydrogen bonding

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strength of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling $\beta$-sheets appearing in native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR

Zero Temperature Glass Transition in the Two-Dimensional Gauge Glass Model

We investigate dynamic scaling properties of the two-dimensional gauge glass model for the vortex glass phase in superconductors with quenched disorder. From extensive Monte Carlo simulations we obtain static and dynamic finite size scaling behavior, where the static simulations use a temperature exchange method to ensure convergence at low temperatures. Both static and dynamic scaling of Monte Carlo data is consistent with a glass transition at zero temperature. We study a dynamic correlation function for the superconducting order parameter, as well as the phase slip resistance. From the scaling of these two functions, we find evidence for two distinct diverging correlation times at the zero temperature glass transition. The longer of these time scales is associated with phase slip fluctuations across the system that lead to finite resistance at any finite temperature, while the shorter time scale is associated with local phase fluctuations.Comment: 8 pages, 10 figures; v2: some minor correction

Opportunities for coupled electrochemical and ion-exchange technologies to remove recalcitrant micropollutants in water

Micropollutants are found in many waters at concentrations that are concerning for living and environmental systems. They are usually characterised as being persistent and are generally difficult to remove from the water using traditional techniques. In this work, we investigate a treatment technology that couples electrooxidation of micropollutants with subsequent absorption of charged products and remaining compounds through a mixed strong acid and strong base ion exchange resin. The results clearly show that carbon fibre is a promising electrode material. Electrooxidation of the drug Ibuprofen using carbon fibre in a coulombic efficiency of 13 mC/ppm removed 71% of the compound after two hours (down to 29 ppm). The addition of sodium chloride led to a near doubling of the pseudo-first order reaction rate from 1.7 to 3.0 10-4 s-1. A mix of Ibuprofen and the pesticide Diuron showed similarly promising results and while the overall oxidation decreased the positive effect of sodium chloride was present. Strikingly, coupling electrooxidation with a mixed bed ion exchange resin removed both compounds, decreasing levels of Diuron to below the limit of detection (18 ppb) and Ibuprofen down to 0.8 ppm. The approach shows potential as a treatment technology for the removal of complex pollutants in water

Novel universality class of absorbing transitions with continuously varying critical exponents

The well-established universality classes of absorbing critical phenomena are directed percolation (DP) and directed Ising (DI) classes. Recently, the pair contact process with diffusion (PCPD) has been investigated extensively and claimed to exhibit a new type of critical phenomena distinct from both DP and DI classes. Noticing that the PCPD possesses a long-term memory effect, we introduce a generalized version of the PCPD (GPCPD) with a parameter controlling the memory effect. The GPCPD connects the DP fixed point to the PCPD point continuously. Monte Carlo simulations show that the GPCPD displays novel type critical phenomena which are characterized by continuously varying critical exponents. The same critical behaviors are also observed in models where two species of particles are coupled cyclically. We suggest that the long-term memory may serve as a marginal perturbation to the ordinary DP fixed point.Comment: 13 pages + 10 figures (Full paper version

Topological Defects in the Random-Field XY Model and the Pinned Vortex Lattice to Vortex Glass Transition in Type-II Superconductors

As a simplified model of randomly pinned vortex lattices or charge-density waves, we study the random-field XY model on square ($d=2$) and simple cubic ($d=3$) lattices. We verify in Monte Carlo simulations, that the average spacing between topological defects (vortices) diverges more strongly than the Imry-Ma pinning length as the random field strength, $H$, is reduced. We suggest that for $d=3$ the simulation data are consistent with a topological phase transition at a nonzero critical field, $H_c$, to a pinned phase that is defect-free at large length-scales. We also discuss the connection between the possible existence of this phase transition in the random-field XY model and the magnetic field driven transition from pinned vortex lattice to vortex glass in weakly disordered type-II superconductors.Comment: LATEX file; 5 Postscript figures are available from [email protected]

Identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling

Activity-based protein profiling is used to screen lignocellulose-degrading enzymes from the white rot fungus Phanerochaete chrysosporium to identify those specifically active in the presence of wood substrate.Activity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.Bio-organic Synthesi

Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome

Mycoplasma genitalium, a human pathogen associated with sexually transmitted diseases, is unique in that it has smallest genome of any known free-living organism. The goal of this study was to investigate if and how M. genitalium uses a minimal genome to generate genetic variations. We analysed the sequence variability of the third gene (MG192 or mgpC) of the M. genitalium MgPa adhesion operon, demonstrated that the MG192 gene is highly variable among and within M. genitalium strains in vitro and in vivo, and identified MG192 sequence shifts in the course of in vitro passage of the G37 type strain and in sequential specimens from an M. genitalium-infected patient. In order to establish the origin of the MG192 variants, we examined nine genomic loci containing partial copies of the MgPa operon, known as MgPar sequences. Our analysis suggests that the MG192 sequence variation is achieved by recombination between the MG192 expression site and MgPar sequences via gene cross-over and, possibly, also by gene conversion. It appears plausible that M. genitalium has the ability to generate unlimited variants from its minimized genome, which presumably allows the organism to adapt to diverse environments and/or to evade host defences by antigenic variation

Author Correction: identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling

Correction to: Communications Biology https://doi.org/10.1038/s42003-022-04141-x, published online 16 November 2022.In the original version of the Article, an incorrect additional description of panel b in Figure 1 was included. The following sentence has now been removed:b Lignocellulose is a complex and recalcitrant polymer built up from cellulose, xylan (hemicellulose), and lignin. Its degradation requires the synergistic action of various different enzymes.Bio-organic Synthesi